Penn State’s Ancient DNA Lab Supports Mammoth Discoveries

Laura: We deal with DNA that is highly degraded and fragmented. DNA rots and decays over time; if your samples are a million years old, you can imagine the amount of decay that has occurred. It’s like trying to assemble a million-year-old puzzle with a million damaged pieces but not having a picture of it to follow.

We can reconstruct DNA from humans, animals, plants, and microorganisms to understand what happened in the past, learn about some of the pitfalls that happened, and apply those lessons to avoid similar ones in the future.

We must work hard to prevent contamination in the lab from modern DNA. We maintain a cleanroom-like sterile environment to reduce contamination by enforcing several controls, such as:

• Setting strict temperature controls for storage and research.
• Undergoing decontamination processes using bleach and ethanol to remove DNA from the outside world.
• Wearing gowns, masks, and eyewear to limit the amount of DNA that people bring into the lab.
• Using ultraviolet (UV) lighting to break down any DNA that enters the lab.

Chad: There are no blueprints for specialized labs such as this one. We relied heavily on communication and collaboration tools to jump on the many challenges we knew were bound to arise. These are some challenges that the Penn State team encountered early in the project schedule:

• Site selection – Our first challenge was for the university to select a suitable site. Finding available space on campus is difficult, and this project’s requirements made site selection particularly challenging. The site needed to be on or close to campus, have suitable building systems, and be isolated from other DNA research to avoid cross-contamination. Ultimately, we selected the Hallowell Building on the university’s west campus.

• Time zones – The researchers were in Australia for most of the design phase, so the 12-hour time difference made for some very early morning or late-night virtual team meetings.
• Project coordination – Within the Hallowell Building, there was already a building-wide HVAC project planned to take place on a similar schedule to the lab. That project fell behind schedule due to various reasons, which created challenges for the lab design team as they tried to integrate design items such as shared ceiling spaces and pipe chases. The team decided to isolate the DNA lab from the other project, which resulted in separate systems and equipment.
• Safety – Some of the lab’s policies were different from what the university’s Environmental Health and Safety Department had encountered before. It was important to engage the department early so they could perform their due diligence.
• Schedule – Construction was scheduled to begin in spring 2020, but the COVID-19 pandemic, subsequent mandatory work stoppage, and supply chain and labor availability issues caused a multi-month delay.
• Operations and maintenance – Because of the sensitivity of the research and the importance of the cleanroom environment, the design team carefully considered accessibility for routine maintenance. To minimize disruptions to the research process, team members identified regular maintenance items and located them in an easy-access area. It was essential to train and communicate with the operations and maintenance staff so they understood the potential impacts on the researchers’ work.

Mike: And these are some challenges the design team tackled as design progressed:

• HVAC – The sensitive nature of the research and the need for a cleanroom-type environment called for very tight environmental controls. It became apparent early in design that the building’s existing HVAC system was inadequate to provide the necessary level of control. An independent HVAC system was installed to regulate temperature and humidity. Also, the lab’s rooms were pressurized to each other and to the rest of the building.
• Power – An emergency generator prevents the research and samples from being compromised by a power outage. The pressure balancing between spaces and the cold storage requirements for samples were among the key factors in the decision to provide emergency power.
• Controls – Access to mechanical equipment by maintenance personnel had to be limited to prevent contamination and interruptions to research. The controls for the lab’s equipment, therefore, were placed remotely in the mechanical penthouse. The project’s complex controls system, custom-developed by Penn State, required a high level of coordination for a successful installation.
• Natural light – One of the highlights of the existing spaces was the abundance of natural light along the north exterior wall. The design team strongly believed that pulling in natural light would provide a more relaxing and pleasant atmosphere for the researchers. Rooms that would be used frequently were located along the exterior wall, while rooms that did not require natural light were located on the corridor side. Interior glazing pulls the natural light farther into the space.

• Transparency – A window into the research suite allows the researchers’ work to be visible to those in the corridor. Passersby and other researchers can watch without disrupting the researchers.
• UV lighting – The lab requires daily cleaning and UV sterilization every evening when the lab is closed. To protect occupants against the hazards of accidental exposure to UV light, the UV system was linked to the occupancy sensor and access control systems. The UV lights are deactivated when the doors are opened, or movement is detected in the space.
• Cleaning – All surface materials withstand rigorous cleaning protocols, including floors, walls, ceilings, casework, countertops, and doors. Ceiling panels have hold-down clips to allow easier cleaning, and floors don’t have joints that could hide contaminants.

Nicole: Coordinating with the design team leaders from the beginning allowed us to make early decisions about things like finishes, lighting, controls, the location of doors and cabinets, removal of anything that might interrupt our workflow, and ways to minimize contamination.

To facilitate communication, we had a direct line to the university personnel. As researchers, we could trust and know that what was being built would work for our research. Communication through calls, emails, and video meetings was key to coordinating all parts of the project.

Chad: Due to the project’s schedule and complexity, the university used its job order contracting method, comprised of preestablished contracts and pricing, allowing us to secure the project’s design and main contractors early. This method proved very beneficial as we worked through the previously mentioned challenges.

It also gave the contractors a better understanding of the project’s goals. With many projects, it seems like when the design is done before the contractors join the team, the contractors build it without understanding the goals and background information. This method allowed us to have a highly collaborative team.

Laura: The lab is a significant resource for the Penn State research community. Penn State is a world leader in interdisciplinary research, and this lab exemplifies that model. Teams from the biology, plant pathology, soil science, and anthropology departments benefit from the lab’s technology.

My team focuses on microorganisms that lived within the body, both helpful and harmful microbes. We’re using ancient DNA to ask questions about the past, including climate change, animal domestication, how infectious diseases were established, and how chronic diseases develop. We’re hoping we can learn from the past to inform the future.

We develop new methods, approaches, and research areas both locally and internationally. We use this lab to research DNA, ancient proteins, metabolites, or chemicals, and explore new mechanisms for understanding the past.

The lab provides a center to train researchers from universities throughout the world that might not have such a facility and create a broader network of DNA researchers. The lab represents an opportunity both here and abroad to research DNA for the benefit of everyone.

To discover the full extent of Gannett Fleming’s commitment to shaping the future through education, explore our diverse portfolio of innovative projects. Visit Gannett Fleming’s Education portfolio to see how we’re making a difference in educational environments.